The Spatial Organization of Human Genome

The 3-dimensional organization of genomes is important for nuclear processes. In mammalian cells, spatial organization of loci relative to each other and to the functional machinery of the nucleus plays an important role in regulation of transcription, replication and DNA repair. Numerous studies have analyzed the role of spatial organization in the function of individual loci. However, due to lack of proper techniques, a genome-wide understanding of chromatin organization is lacking. By combining the basic principles of Chromosome Conformation Capture (3C) with massively parallel sequencing, we have devised a method called "Tethered Conformation Capture" (TCC) that enables analysis of spatial organization of genomes in an unbiased fashion. TCC employs solid-phase ligation to capture genomic contacts, thereby reducing random intermolecular ligations and resulting false-positive contacts compared to solution-based approaches. This improvement in the signal-to-noise ratio facilitates the analysis of low frequency contacts. TCC also provide a platform for automated and high throughput analysis of the 3D conformation of mammalian genome. The data generated by TCC reflects the chromatin interactions in the form of binary contacts between loci at high resolution. We have analyzed the basic characteristics of spatial organization of the human genome such as chromosome territories and contact probability distribution. With respect to the functional organization of the genome, the data shows that chromosomes can be divided into functionally active and inactive regions that show opposite patterns of binary contacts. We have further characterized the association patterns of active and inactive regions and found that these patterns reflect their three-dimensional organization. We have also studied the underlying principles of intermingling between loci that belong to different chromosome territories. Knowledge of the spatial organization of gene loci in the nucleus may help elucidating the principles that underlie gene regulatory processes. Here we show how integration of data from tethered conformation capture experiments can be used to determine the spatial organization of the human genome. The process involves collection of sufficient and diverse data, translation of this data into spatial restraints, and an optimization that uses these restraints to generate a population of genome structures that is consistent with the data. Analysis of this population produces an architectural map of the genome, where the locations of chromosome regions can be described by spatial distribution functions. Our model detects co-localization patterns of specific chromosomes and predicts radial positions of chromosome territories that are in agreement with independent experimental data.